Journal ArticleDOI
MITOS: Improved de novo metazoan mitochondrial genome annotation
Matthias Bernt,Alexander Donath,Frank Jühling,Frank Jühling,Fabian Externbrink,Catherine Florentz,Guido Fritzsch,Joern Pütz,Martin Middendorf,Peter F. Stadler +9 more
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TLDR
The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences and it is shown that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2013-11-01. It has received 3323 citations till now. The article focuses on the topics: RefSeq.read more
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The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae)
TL;DR: A robust glycerid phylogeny is resolved and three clades are identified comprising the majority of taxa, with group II introns inside the cox1 gene of two analyzed glycerids specimens, with two different insertions in one of these species.
Journal ArticleDOI
Characterization and comparative mitogenomic analysis of six newly sequenced mitochondrial genomes from ectomycorrhizal fungi (Russula) and phylogenetic analysis of the Agaricomycetes.
Qiang Li,Qiangfeng Wang,Cheng Chen,Xin Jin,Zuqin Chen,Chuan Xiong,Ping Li,Jian Zhao,Wenli Huang +8 more
TL;DR: This study provides the first report of mitogenomes from the Russulaceae family and facilitates the investigation of population genetics and evolution of other ectomycorrhizal fungi.
Journal Article
Chloroplot: an online program for the versatile plotting of organelle genomes
TL;DR: An online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes, which allows the depiction of the codon usage bias index for each gene.
Journal ArticleDOI
Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition
Mun Hua Tan,Han Ming Gan,Yin Peng Lee,Heather D. Bracken-Grissom,Tin-Yam Chan,Adam D. Miller,Christopher M. Austin +6 more
TL;DR: Predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships, and several clade-specific trends that are of evolutionary and ecological interest are indicated.
Journal ArticleDOI
Puma genomes from North and South America provide insights into the genomic consequences of inbreeding
Nedda F. Saremi,Megan A. Supple,Ashley Byrne,James A. Cahill,James A. Cahill,Luiz Lehmann Coutinho,Love Dalén,Henrique V. Figueiró,Warren E. Johnson,Warren E. Johnson,Heather J. Milne,Stephen J. O'Brien,Brendan O'Connell,Brendan O'Connell,David P. Onorato,Seth P. D. Riley,Jeff A. Sikich,Daniel R. Stahler,Priscilla Marqui Schmidt Villela,Christopher Vollmers,Robert K. Wayne,Eduardo Eizirik,Russell Corbett-Detig,Richard E. Green,Christopher C. Wilmers,Beth Shapiro,Beth Shapiro +26 more
TL;DR: It is found that tracts of homozygosity are rarely shared among geographically isolated North American populations, suggesting that assisted gene flow would restore local genetic diversity, and that sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
Journal ArticleDOI
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock,Tiago Antao,Jeffrey T. Chang,Brad Chapman,Cymon J. Cox,Andrew Dalke,Iddo Friedberg,Thomas Hamelryck,Frank Kauff,Bartosz Wilczyński,Michiel J. L. de Hoon +10 more
TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Journal ArticleDOI
Automatic annotation of organellar genomes with DOGMA
TL;DR: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
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